BN1910 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 2.6458e-05 7.8831e-04
WM 1.1734e-04 2.9190e-02
Layer 4 3.1802e-04 6.0586e-03
Layer 2 5.1172e-04 3.6126e-03
Layer 5 1.1753e-03 6.2339e-02
Layer 6 1.4245e-03 2.0425e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PRKAR1A Expression Distribution
Gene Specificity Score (GSS)
PRKAR1A GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PRKAR1A Layer 3 2.2617 0.5881
SNCA Layer 6 1.8926 0.5877
ATP1B1 Layer 3 2.3965 0.5815
MGST3 Layer 3 2.3154 0.5793
OAZ1 Layer 3 2.2832 0.5769
GPX4 Layer 3 2.2578 0.5743
RTN3 Layer 3 2.3027 0.5740
GDI1 Layer 2 2.3027 0.5718
HINT1 Layer 2 2.3027 0.5667
COX6C Layer 2 2.5273 0.5665
RABAC1 Layer 3 2.1680 0.5613
CFL1 Layer 3 2.1582 0.5588
SLC22A17 Layer 3 2.3867 0.5567
CHCHD2 Layer 3 2.1904 0.5558
ARF1 Layer 3 2.3965 0.5542
AP2M1 Layer 4 2.2129 0.5500
GRINA Layer 3 2.2676 0.5495
SARAF Layer 2 2.2324 0.5487
SOD1 Layer 3 2.1777 0.5480
ATP6V0B Layer 3 2.2227 0.5480
ATP5MD Layer 3 2.4844 0.5477
NDUFA3 Layer 3 2.3125 0.5475
NDFIP1 Layer 3 2.7188 0.5472
DYNLRB1 Layer 3 2.1289 0.5471
APP Layer 3 2.2168 0.5458
DYNLL1 Layer 2 2.1348 0.5456
DSTN Layer 2 2.6777 0.5456
CAPNS1 Layer 3 2.0820 0.5454
SERINC1 Layer 2 2.3652 0.5452
TXN Layer 3 1.9805 0.5442
UQCR10 Layer 2 2.4844 0.5429
COX5B Layer 3 2.2832 0.5423
PEBP1 Layer 3 2.2031 0.5411
BEX3 Layer 3 2.3438 0.5406
FAIM2 Layer 2 2.6602 0.5403
COX7B Layer 2 2.4785 0.5402
EEF2 Layer 3 2.1348 0.5402
RPS26 Layer 3 2.0859 0.5400
ATP6V1E1 Layer 2 2.4336 0.5386
YWHAE Layer 3 2.0586 0.5356
SKP1 Layer 3 2.2832 0.5354
RPL14 Layer 4 2.1055 0.5351
COX6A1 Layer 3 2.2168 0.5351
BNIP3 Layer 3 2.1221 0.5348
FKBP8 Layer 3 2.1719 0.5346
EIF4G2 Layer 2 2.2715 0.5344
ATP6V0C Layer 3 2.2490 0.5341
SLC24A2 Layer 3 2.4121 0.5337
CKB Layer 2 2.1719 0.5334
PRNP Layer 2 2.1680 0.5333

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1910
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1910_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1910/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1910/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1910/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1910/report/PD/BN1910_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1910/report/PD/BN1910_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:39:27
  • Number of Processes: 10
  • Spending Time: 0h 4m